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Bug #22695

open

arvados-cwl-runner depends on older version of cwltool & schema-salad; prevents installation under Python 3.13

Added by Michael Crusoe about 1 year ago. Updated about 2 months ago.

Status:
New
Priority:
Normal
Assigned To:
Category:
CWL
Target version:
-
Story points:
-
Release relationship:
Auto

Description

To reproduce, in a fresh Python 3.13 virtualenv, pip install schema-salad arvados-cwl-runner

Similarily, forcing the installation of the latest arvados-cwl-runner (3.1.0) fails under Python 3.13

pip install arvados-cwl-runner==3.1.0
Collecting arvados-cwl-runner==3.1.0
  Using cached arvados_cwl_runner-3.1.0-py3-none-any.whl.metadata (4.0 kB)
Collecting arvados-python-client==3.1.0 (from arvados-cwl-runner==3.1.0)
  Using cached arvados_python_client-3.1.0-py3-none-any.whl.metadata (4.1 kB)
Collecting ciso8601>=2.0.0 (from arvados-cwl-runner==3.1.0)
  Using cached ciso8601-2.3.2-cp313-cp313-linux_x86_64.whl
Collecting crunchstat-summary==3.1.0 (from arvados-cwl-runner==3.1.0)
  Using cached crunchstat_summary-3.1.0-py3-none-any.whl.metadata (437 bytes)
Collecting cwltool==3.1.20240508115724 (from arvados-cwl-runner==3.1.0)
  Using cached cwltool-3.1.20240508115724-py3-none-any.whl.metadata (40 kB)
INFO: pip is looking at multiple versions of arvados-cwl-runner to determine which version is compatible with other requirements. This could take a while.
ERROR: Ignored the following yanked versions: 8.3.20220721194857
ERROR: Could not find a version that satisfies the requirement schema-salad==8.5.20240503091721 (from arvados-cwl-runner) (from versions: 1.0, 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.0.6, 1.1.0, 1.1.1, 1.2.20151210153655, 1.3.20160108151816, 1.4.20160108152457, 1.4.20160108200836, 1.5.20160126150511, 1.5.20160126190004, 1.5.20160126213649, 1.6.20160202222448, 1.7, 1.7.20160315232142, 1.7.20160316145902, 1.7.20160316150109, 1.7.20160316203940, 1.9.20160421133216, 1.10.20160505184637, 1.10.20160505185111, 1.11.20160506154702, 1.11.20160524152859, 1.12.20160610092802, 1.12.20160610104117, 1.13.20160630144631, 1.13.20160702001514, 1.14.20160707164023, 1.14.20160708181155, 1.15.20160810152809, 1.16.20160810195039, 1.16.20160819133325, 1.17.20160820165726, 1.17.20160820171034, 1.18.20160907135919, 1.18.20160930145650, 1.18.20161005190847, 1.20.20161122192122, 1.21.20161202201331, 1.21.20161206181442, 1.21.20161206204028, 1.21.20161215163938, 2.0.20161122040508, 2.1.20161216210732, 2.1.20161221160224, 2.1.20161223160831, 2.1.20161227191302, 2.2.20170111180227, 2.2.20170119151016, 2.2.20170126160727, 2.2.20170208112505, 2.2.20170216125639, 2.2.20170222151604, 2.3.20170302150835, 2.3.20170302225134, 2.4.20170308171942, 2.5.1.20170628121527, 2.5.20170327140858, 2.5.20170328195758, 2.5.20170428142041, 2.5.20170623152720, 2.6.20170628130600, 2.6.20170630075932, 2.6.20170712194300, 2.6.20170806163416, 2.6.20170927145003, 2.6.20171031091636, 2.6.20171101113912, 2.6.20171102064032, 2.6.20171116190026, 2.6.20171201034858, 2.6.20180214144209, 2.7.20180302220026, 2.7.20180322174040, 2.7.20180501211602, 2.7.20180514111532, 2.7.20180514132321, 2.7.20180611133406, 2.7.20180717111941, 2.7.20180719125426, 2.7.20180724081820, 2.7.20180731120629, 2.7.20180809223002, 2.7.20180905124720, 2.7.20181012180226, 2.7.20181017120439, 2.7.20181116024232, 2.7.20181126142424, 3.0.20181129082112, 3.0.20181206233650, 3.1.20190125161400, 4.0.20190130225346, 4.1.20190221213919, 4.1.20190227145202, 4.1.20190305210046, 4.2.20190417121603, 4.3.20190603183756, 4.3.20190604170443, 4.4.20190620173027, 4.5.20190621200723, 4.5.20190729164411, 4.5.20190815125611, 4.5.20190906201758, 4.5.20191017101802, 4.5.20191023134839, 4.5.20191203162929, 4.5.20191204060541, 4.5.20191229160203, 5.0.20200105154004, 5.0.20200122085940, 5.0.20200126033820, 5.0.20200220195218, 5.0.20200302192450, 5.0.20200416112825, 6.0.20200523200656, 6.0.20200601095207, 7.0.20200612160654, 7.0.20200811075006, 7.0.20201119201711, 7.0.20210124093443, 7.1.20210309094900, 7.1.20210316164414, 7.1.20210518142926, 7.1.20210611090601, 8.0.20210624094941, 8.0.20210624101613, 8.0.20210624154013, 8.1.20210627200047, 8.1.20210716111910, 8.1.20210721123742, 8.2.20210902094147, 8.2.20210914115719, 8.2.20210918131710, 8.2.20211014142459, 8.2.20211014150008, 8.2.20211015115235, 8.2.20211020114435, 8.2.20211029004247, 8.2.20211103155537, 8.2.20211104054942, 8.2.20211116214159, 8.2.20211222191353, 8.2.20220103095339, 8.2.20220204150214, 8.3.20220518163624, 8.3.20220525163636, 8.3.20220626094427, 8.3.20220626185350, 8.3.20220717021618, 8.3.20220717184004, 8.3.20220801194920, 8.7.20240905150001, 8.7.20241010092723, 8.7.20241021092521, 8.8.20241204110045, 8.8.20241206093842, 8.8.20250205075315)
ERROR: No matching distribution found for schema-salad==8.5.20240503091721

Files

22695-try1.patch (1.7 KB) 22695-try1.patch Brett Smith, 09/19/2025 01:47 PM
update-cwltool.log (21.1 KB) update-cwltool.log Brett Smith, 09/19/2025 01:47 PM

Related issues 1 (1 open0 closed)

Blocks Arvados Epics - Idea #23170: Add support for Debian 13 (trixie)NewActions
Actions #1

Updated by Peter Amstutz 10 months ago

  • Target version set to Development 2025-06-25
Actions #2

Updated by Peter Amstutz 10 months ago

  • Release set to 79
Actions #3

Updated by Peter Amstutz 10 months ago

  • Target version changed from Development 2025-06-25 to Development 2025-07-09
Actions #4

Updated by Peter Amstutz 10 months ago

  • Category set to CWL
Actions #5

Updated by Peter Amstutz 10 months ago

  • Target version changed from Development 2025-07-09 to Development 2025-07-23
Actions #6

Updated by Peter Amstutz 10 months ago

  • Target version changed from Development 2025-07-23 to Future
Actions #7

Updated by Brett Smith 6 months ago

  • Blocks Idea #23170: Add support for Debian 13 (trixie) added

Updated by Brett Smith 6 months ago

Took a quick look to see if this would be easy to knock out. See patch and test log attached. Something about the way we're resolving CUDARequirements changed and will need to be updated. Note the test failures happen before we even get to an assert; it's possible we just need to update mocks.

Actions #9

Updated by Brett Smith 4 months ago

The test failure is real and happens because of a bug in cwltool: https://github.com/common-workflow-language/cwltool/issues/2114

Unfortunately this means our own Python 3.13/Debian 13 support is blocked on a fix and release. :/

Actions #10

Updated by Brett Smith 3 months ago ยท Edited

  • Target version set to Development 2026-01-06
  • Assigned To set to Brett Smith

Hopefully fixed upstream by this commit - needs testing.

Actions #11

Updated by Brett Smith 3 months ago

  • Target version changed from Development 2026-01-06 to Development 2026-01-21
Actions #12

Updated by Brett Smith 2 months ago

  • Target version changed from Development 2026-01-21 to Development 2026-02-04
Actions #13

Updated by Brett Smith about 2 months ago

  • Release changed from 83 to 81
  • Target version deleted (Development 2026-02-04)
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